Thermodynamics ∆Euniverse = 0 ∆Suniverse > 0 ∆Ssystem + ∆Ssurroundings = ∆Suniverse ∆G = ∆H – T∆S At equilibrium ∆G = 0 ∆H (energy required to break bonds) – (energy released during bond formation). ∆G<0 is spontaneous (exergonic); ∆G>0 is non-spontaneous (endergonic); ∆G represents the maximum possible amount of useful energy obtainable from a reaction). ∆G is totally unrelated to rate. ∆G° is relative stability of starting and ending states. ∆G depends on ∆G° and conditions. # [Products] & [C][D] ∆G° = –RTlnKeq "G = "G° + RT ln% A+B C + D K eq = ( [A][B] $ [Reactants] ' ∆G´°: pH = 7.0; [H2O] is part of ∆G´°, and [Mg2+] = 1 mM. For reactions in which water and H+ are not reactants, ∆G´° = ∆G°. ! Solubility ! in water (and other solvents) depends on ∆H and ∆S terms. The hydrophobic effect is largely due to ∆Swater. kq q Ionic solutes – water is a protic solvent; it stabilizes both cations and F = 12 2 anions. "r [A – ] Acid-base properties of inorganic and organic compounds: pH = pK a + log If an [HA] acid is added to a solution, the pH will decrease. If a base is added!to a solution, the pH will increase. Buffers attenuate the pH change by binding or releasing protons. ! the charge on an amino acid or Amino acids are always ionized in aqueous solution; protein depends on the nature of the group(s) and the degree of protonation. The local environment alters the pKa values for ionizable groups. Primary (1°) Structure – Covalent backbone and amino acid sequence Secondary (2°) Structure – Hydrogen bonding for backbone atoms Tertiary (3°) Structure – 3D structure: hydrophobic effect, H-bonds, electrostatic interactions, van der Waals interactions (favorable and unfavorable due to steric constraints, especially for peptide bond), and (relatively rare) disulfide bonds. Quaternary (4°) Structure – Multichain proteins: non-covalent and (in surface/extracellular proteins) disulfide interactions between polypeptides. Secondary structure is a way of stabilizing the polar peptide backbone; secondary structures are repeating Φ / Ψ angle pairs. Real secondary structures frequently do not have exactly the angles shown below. Parameter Φ Ψ rise per residue α-Helix Antiparallel Parallel β-sheet β-sheet Collagen –57° –139° –119° –51° –47° 1.5 Å (3.6 residues/turn) 135° 3.5 Å 113° 3.5 Å 153° 3 Å (3.3 residues/turn) Proteins are stable because of thermodynamic and/or kinetic considerations. Proteinunfolded Polar residues ΔHchain ΔHsolvent ΔHchain Non-polar residues (+) (–) small (+) or small (–) (–) significant ΔHsolvent COO- COO- + H3 C (+) (–) (+) (–T∆Ssolvent) (–) large COO+ H3 N C H CH3 H3 N C H CH3 H3C C H3 COO- COO- COO- H3 N C H H3 N C H H3 N C H + + COO- COO- OH H3 C O COO- COO- + OH COO+ H3 N C H NH2 + NH3 O N H COO+ H3 N C H R2 O R3 O + H3 N C C N C C N C C O H H H #+ N H NH2 COO- + H3 N C H ! " #$ R1 O SH + H3 N C H H3 N C H O NH2 H3 N C H OH + H3 N C H O + COO- + O COO- + H3 N C H H3 N C H H3 N C H O C H COO- + COONH2 H2 N H + H3 N C H CH3 COO+ H3 N C H + COO- S + N H + for folding + H3 N C H CH3 Overall ∆G > 0 for folding Overall ∆G < 0 COO- + H3 N C H CH3 (–T∆Schain) (–T∆Ssolvent) (–T∆Schain) COO- + H3 N C H Proteinfolded + N N H NH H H Carbohydrates are usually chiral molecules; monosaccharides have a general molecular formula Cn(H2O)n. The linear form contains a carbonyl (aldehyde or 2ketone); monosaccharides with 5 or more carbons form cyclic hemiacetals in aqueous solution.